{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28558722", "kind": "science-record", "revision": 4, "content_hash": "sha256:8d92af5c0061283cf819dbe6197188f7cd95da3d1742198a40ba4dac28af22a7", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T21:20:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms.", "doi": "10.1186/s12862-017-0973-4", "pmid": "28558722", "authors": ["Frank E Anderson", "Bronwyn W Williams", "Kevin M Horn", "Christer Erséus", "Kenneth M Halanych", "Scott R Santos", "Samuel W James"], "journal": "BMC evolutionary biology", "year": 2017, "abstract": "BACKGROUND: Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved.\nMETHODS: In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion.\nRESULTS AND DISCUSSION: We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea.\nCONCLUSIONS: These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.", "claims": [{"id": "claim-method", "statement": "both a SOWH test and a Bayesian topology test strongly reject Dichogaster monophyly.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28558722", "locator": "sections[18] \"Crassiclitellata systematics\" paragraph 6", "quote": "both a SOWH test and a Bayesian topology test strongly reject Dichogaster monophyly."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28558722", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study recovered a consistent, strongly supported earthworm topology irrespective of methodology, using four gene sets and Bayesian CAT-GTR analyses, while its newly generated transcriptomes are available through NCBI’s Sequence Read Archive under BioProject PRJNA362879 and its two public datasets are identified by PRJNA196484 and PRJDB3115.", "kind": "quantitative", "target": {"value": 75.0, "unit": "per cent", "tolerance": null, "source": "Bayesian analyses under the CAT-GTR model were attempted for the unfiltered 25, 50, and 75% data sets and the two filtered “no ?Haplotaxidae sp.” 75% matrices in PhyloBayes"}, "evidence": [{"asset": "source:pmid:28558722", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology."}, {"asset": "source:pmid:28558722", "locator": "sections[12] \"Results\" paragraph 2", "quote": "Four gene sets from these transcriptomes were analyzed, reflecting different levels of gene occupancy."}, {"asset": "source:pmid:28558722", "locator": "sections[13] \"Ingroup relationships\" paragraph 4", "quote": "Bayesian analyses under the CAT-GTR model were attempted for the unfiltered 25, 50, and 75% data sets and the two filtered “no ?Haplotaxidae sp.” 75% matrices in PhyloBayes"}, {"asset": "source:pmid:28558722", "locator": "sections[12] \"Results\" paragraph 2", "quote": "Transcriptomes for thirty-one crassiclitellates, one moniligastrid, and six outgroup taxa were generated as part of this study (Table 1; Additional file 1: Figure S1) and are available from the SRA at NCBI under BioProject accession number PRJNA362879."}, {"asset": "source:pmid:28558722", "locator": "sections[12] \"Results\" paragraph 2", "quote": "We added publicly available transcriptome data for two additional crassiclitellates—Hormogaster elisae (PRJNA196484) and Eisenia andrei (PRJDB3115)—for a total of forty transcriptomes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study recovered a consistent, strongly supported earthworm topology irrespective of methodology, using four gene sets and Bayesian CAT-GTR analyses, while its newly generated transcriptomes are available through NCBI’s Sequence Read Archive under BioProject PRJNA362879 and its two public datasets are identified by PRJNA196484 and PRJDB3115.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28558722"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJDB3115"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJDB3115"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28558722", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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number of Illumina reads, number of Trinity contigs and number of HaMSTr ortholog groups represented for each of the thirty-seven transcriptomes generated in this study", "structure": {"pmcid": "PMC5450073", "section_index": 3, "section_title": "Taxon sampling", "row_count": 42, "column_count": 5}, "table": {"label": "Table 1", "caption": "Collection locality, museum location of voucher specimen, museum catalog number, SRA project number, number of Illumina reads, number of Trinity contigs and number of HaMSTr ortholog groups represented for each of the thirty-seven transcriptomes generated in this study", "rows": [["Taxon", "Locality", "Museum", "# Contigs", "# HaMStR Orthologs"], ["Acanthodrilidae sp.", "Argentina, Tierra del Fuego, Ushuaia (coll. E. Lapied)", "NCSM 27264", "181228", "1140"], ["Alma sp.Almidae", "Gabon, edge of Lac Vembo, Gamba complex, (coll. S James 18 May 2008)", "NCSM 27265", "110015", "558"], ["Avelona ligra Lumbricidae", "France, Jargeau, Loiret Department, (coll. M. Koken)", "MNHN XXXXXX", "182509", "1173"], ["Criodrilus lacuum Criodrilidae", "Hungary (coll. C. Csuzdi)", "NCSM 27266", "119084", "934"], ["Dendrobaena hortensis Lumbricidae", "Sweden, Södermanland, Vingåker, Valltrand, indoor compost, 59.0864 N, 16.0544 E (coll. E. Boräng, 1 Jan 2012)", "SMNH 161291in EtOH CE13942", "179981", "1180"], ["Dichogaster sp. (green tree worm) Benhamiidae", "Brazil, Amazonas, near Manaus, Reserva Campina (coll. S. James, S. Coral, 2 Feb 2012)", "NCSM 27267", "116065", "1140"], ["Dichogaster sp.Benhamiidae", "France, Guadeloupe, Basse Terre (colls. S. James, F. Gamiette Feb 2013)", "NCSM 27268", "106438", "1152"], ["Dichogaster saliens Benhamiidae", "France, Guadeloupe, Chutes Carbet, Basse Terre (colls. S. James, F. Gamiette Feb 2013)", "NCSM 00000", "98665", "999"], ["Drawida sp.Moniligastridae", "USA, Tonganoxie, Kansas (coll. S. James? May 2013)", "NCSM 27269", "159219", "1081"], ["Eisenia andrei Lumbricidae", "Unknown", "---", "137631", "1217"], ["Eisenia andrei Lumbricidae", "Sweden, Södermanland, Vingåker, Valltrand, indoor compost, 59.0864 N, 16.0544 E (coll. E. Boräng, 1 Jan 2012)", "SMNH 161292in EtOH CE13945", "168836", "1191"], ["Eudrilus eugeniae Eudrilidae", "Brazil, Sao Paulo, bait shop (coll. S. James, 7 Nov 2010)", "NCSM 27270", "85990", "1008"], ["Fimoscolex sp.Glossoscolecidae", "Brazil, Assistencia, São Paulo, Fazenda Sta Rosa (coll. S. James, 9 Nov 2012)", "NCSM 27271", "95465", "705"], ["Gatesona chaetophora Lumbricidae", "France, Aveyron, L'Hospitalet du Larzac (coll. S James, 1 Mar 2011)", "NCSM 27272", "104334", "961"], ["Geogenia benhami Microchaetidae", "South Africa, Western Cape, Stellenbosch (colls S. James, D. Plisko, 27 Aug 2011)", "NCSM 27273", "84303", "932"], ["Glossodrilus sp.Glossoscolecidae", "Brazil, Amazonas, near Manaus, Reserva Ducke (colls. S. James, S. Coral 1 Feb 2012)", "NCSM 27274", "122993", "1053"], ["Glossoscolex sp.Glossoscolecidae", "Brazil, Parana, Campina Grande do Sul, Caratuva peak trail (coll. S. James, M. Bartz, 17 Oct 2010)", "NCSM 27275", "58411", "722"], ["Hemigastrodrilus monicae Hormogastridae", "France, Aveyron, L'Hospitalet du Larzac (coll. S James, 1 Mar 2011)", "NCSM 27276", "103338", "1098"], ["Hormogaster elisae Hormogastridae", "SRA PRJNA196484*,Spain, El Molar, 40°44′22.9″N, 3°33′53.1″W", "---", "459282", "1234"], ["Kerriona sp. Graciosa1Ocnerodrilidae", "Brazil, Parana, Graciosa Road (coll. S. James, 4 Nov 2010)", "NCSM 27277", "104982", "1010"], ["Komarekiona eatoni Komarekionidae", "USA, Sideling Hill Wildlife Mgmt. Area, Washington County, Maryland. (colls. S. James, M. Callaham, May 2013)", "NCSM 27278", "83743", "1151"], ["Kynotus pittarelli Kynotidae", "Madagascar, Antsirabe, 19°46'38.60\"S 47°06'41.69\"E", "NCSM 00000", "108836", "1073"], ["Lutodrilus multivesiculatus Lutodrilidae", "USA, Louisiana, Washington Parish (coll S. James, M. Callaham, M. Damoff, C. Erseus, 17 Jan 2011)", "NCSM 00000", "57341", "1049"], ["Maoridrilus wilkini Acanthodrilidae", "New Zealand, Kelly’s Creek (coll. T. Buckley)", "NCSM 27279", "80910", "861"], ["Microchaetidae sp.", "South Africa, Western Cape, Tokai Swamp (colls. S. James and D. Plisko, 29 Aug 2011)", "NCSM 27280", "194638", "1053"], ["Microchaetus sp.Microchaetidae", "South Africa, Northern Cape, Niewwoudtville (colls. S. James, D. Plisko 5 Sep 2011)", "NCSM 27281", "125494", "1093"], ["Parachilota sp.Acanthodrilidae", "South Africa, Western Cape, Table Mountain (coll. James, Meassey, Plisko, 26 Aug 2011)", "NCSM 27282", "102971", "1074"], ["Place Kabary 2 sp.Acanthodrilidae", "Madagascar, Place Kabary, Antsiranana, 12°16'58.27''S 49°17'25.94''E", "NCSM 00000", "146018", "1157"], ["Pontodrilus litoralis Megascolecidae", "USA, Cedar Point, Alabama (colls. S. James, C. Erséus 17 January 2011)", "NCSM 00000", "90268", "1189"], ["Rhinodrilus priollii Rhinodrilidae", "Brazil, Amazonas, Reserve Ducke (colls. S. James, S. Coral, 3 Feb 2012)", "NCSM 00000", "87158", "1102"], ["Scherotheca savignyi Lumbricidae", "France, Midi-Pyrénées, Ariège, Malegoude (coll. S. James, 2 Mar 2011)", "NCSM 27283", "113157", "1041"], ["Sparganophilus sp.Sparganophilidae", "USA, Iowa, Des Moines River, at Douds (coll. S. James 12 May 2012)", "NCSM 27284", "123905", "1199"], ["Urobenus brasiliensis Rhinodrilidae", "Brazil, Rio Grande do Sul, Santo Cristo (coll. G. Steffen 09 Sep 2009)", "NCSM 27285", "55709", "890"], ["Vignysa popi Hormogastridae", "France, Aveyron, Montpellier (colls. S. James, M. Bouche, 1 Mar 2011)", "NCSM 27286", "93260", "779"], ["Outgroups"], ["Delaya leruthi Haplotaxidae", "France, Midi-Pyrénées, Ariège, Cazavet, L'Estelas Cave, in water, 43.000 N, 1.010 E (coll. M.C. des Chatelliers, P. Martin & N. Giani, 24 May 2011) (topotype)", "SMNH 161293in EtOH CE13924", "118020", "1067"], ["Pelodrilus sp.Haplotaxidae", "Western Australia, 25.5 km S of Busselton, Rapids Conservation Park, Margaret River (coll. C. Erséus, 16 Sep 2012)", "WAM V9004", "100864", "1129"], ["Haplotaxis gordioides Haplotaxidae", "Sweden, Västergötland, Göteborg, seeping groundwater at Göteborg Botanical Garden (Vitsippsdalen), 57.6813 N, 11.9562 E (C. Erséus & A. Achurra, 29 Mar 2011)", "SMNH 161294 in EtOH CE11200", "53878", "855"], ["?Haplotaxidae sp.", "Brazil, Amazonas, Reserva Ducke (colls. S. James, S. Coral, 3 Feb 2012) (topotype)", "NCSM 000000 in EtOH CE14372", "93548", "1053"], ["Lumbriculus variegatus Lumbriculidae", "Sweden, Västergötland, Göteborg, Guldheden, spring S of Dr Fries Torg, 57.6827 N, 11.9707 E (coll. M. Svensson, 8 Nov 2011)", "SMNH 161295 slide CE13679", "109949", "985"], ["Propappus volki Propappidae", "Sweden, Blekinge, Ronneby, Väby, Bräkneån River, sand in rapids, 56.1792 N, 15.1052 E (C. Erséus, B. Williams & S. Martinsson, 31 May 2013) (topotype)", "SMNH 161296 slide CE18375", "131574", "1140"]], "row_count": 42, "column_count": 5, "numeric_cells": 153, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:28558722:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:470085a87fd890d0731356f1605c5fb5b1aa3326f70e2d0a07f7cd9d13c79e89", "bytes": 1102, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab2", "version": null, "note": "Characteristics of all data matrices analyzed in this study", "structure": {"pmcid": "PMC5450073", "section_index": 7, "section_title": "Long-branch effects and compositional heterogeneity", "row_count": 17, "column_count": 5}, "table": {"label": "Table 2", "caption": "Characteristics of all data matrices analyzed in this study", "rows": [["Data Set", "# Loci", "# Characters", "# Parsimony-informative Characters", "% Missing"], ["25%"], ["Unpartitioned/partitioned original data", "766", "361,365", "64,892", "77.27"], ["TreSpEx + BaCoCa filtered", "543", "251,614", "40,509", "77.56"], ["Deleted outgroups", "727", "337,650", "59,520", "76.97"], ["50%"], ["Unpartitioned/partitioned original data", "162", "58,085", "18,515", "55.57"], ["TreSpEx + BaCoCa filtered", "131", "46,468", "15,173", "53.29"], ["Deleted outgroups", "206", "78,060", "22,753", "55.34"], ["75%"], ["Unpartitioned/partitioned original data", "58", "16,458", "6596", "35.21"], ["TreSpEx + BaCoCa filtered", "49", "14,075", "5785", "34.99"], ["Deleted outgroups", "92", "28,097", "9844", "35.00"], ["No ?Haplotaxidae sp., all sites", "56", "16,541", "6879", "33.45"], ["No ?Haplotaxidae sp., no gappy sites", "56", "13,168", "6443", "18.62"], ["100%"], ["Unpartitioned/partitioned original data", "7", "1997", "805", "20.21"]], "row_count": 17, "column_count": 5, "numeric_cells": 52, "header_rows": 1, "locator": "section[7]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:28558722:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1a6c5b1e05b963435ceceb63490461842ad10a2b69e6292f644c39f91798179e", "bytes": 5103, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab3", "version": null, "note": "Percent missing data per taxon across all matrices analyzed in this study, calculated using TREE-PUZZLE 5.3", "structure": {"pmcid": "PMC5450073", "section_index": 13, "section_title": "Ingroup relationships", "row_count": 42, "column_count": 13}, "table": {"label": "Table 3", "caption": "Percent missing data per taxon across all matrices analyzed in this study, calculated using TREE-PUZZLE 5.3", "rows": [["", "Matrix"], ["Taxon", "25 U", "25 T", "25D", "50 U", "50 T", "50D", "75 U", "75 T", "75D", "75H", "75HG", "100 U"], ["Acanthodrilidae sp.", "71.28", "70.48", "71.28", "49.23", "48.86", "49.23", "24.94", "48.86", "24.94", "25.32", "8.29", "16.62"], ["Alma sp.", "93.52", "93.39", "93.52", "84.99", "84.61", "84.99", "71.86", "84.61", "71.86", "73.99", "68.13", "44.37"], ["Avelona ligra", "70.46", "67.95", "70.46", "47.68", "42.17", "47.68", "26.91", "42.17", "26.91", "23.52", "6.48", "14.97"], ["Criodrilus lacuum", "84.72", "84.45", "84.72", "62.46", "57.70", "62.46", "44.00", "57.70", "44.00", "44.02", "31.04", "20.93"], ["Delaya leruthi", "78.74", "82.55", "78.74", "52.10", "50.12", "52.10", "28.27", "50.12", "28.27", "29.27", "14.19", "16.88"], ["Dendrobaena hortensis", "70.35", "69.16", "70.35", "44.63", "39.30", "44.63", "23.86", "39.30", "23.86", "18.36", "2.59", "12.52"], ["Dichogaster sp. (green tree worm)", "71.97", "70.21", "71.97", "54.66", "53.56", "54.66", "29.06", "53.56", "29.06", "24.36", "7.03", "17.93"], ["Dichogaster sp.", "69.76", "67.77", "69.76", "50.28", "49.08", "50.28", "27.37", "49.08", "27.37", "24.48", "7.49", "16.07"], ["Dichogaster saliens", "80.45", "78.88", "80.45", "63.13", "62.73", "63.13", "34.41", "62.73", "34.41", "27.56", "11.44", "17.63"], ["Drawida sp.", "78.41", "80.37", "78.41", "57.60", "55.64", "57.60", "39.68", "55.64", "39.68", "39.08", "25.80", "15.82"], ["Eisenia andrei", "62.78", "62.04", "62.78", "39.83", "37.24", "39.83", "25.17", "37.24", "25.17", "23.14", "5.07", "16.07"], ["Eisenia andrei SRA", "69.12", "66.93", "69.12", "43.18", "38.61", "43.18", "25.96", "38.61", "25.96", "21.76", "4.33", "19.93"], ["Eudrilus eugeniae", "79.96", "80.02", "79.96", "58.95", "57.36", "58.95", "31.73", "57.36", "31.73", "31.96", "15.98", "23.99"], ["Fimoscolex sp.", "88.37", "87.75", "88.37", "76.41", "75.80", "76.41", "56.96", "75.80", "56.96", "61.63", "52.16", "31.90"], ["Gatesona chaetophora", "79.32", "78.45", "79.32", "54.76", "49.42", "54.76", "27.69", "49.42", "27.69", "23.66", "7.19", "15.42"], ["Geogenia benhami", "83.35", "84.86", "83.35", "62.53", "57.10", "62.53", "38.68", "57.10", "38.68", "41.06", "27.62", "19.83"], ["Glossodrilus sp.", "76.14", "75.65", "76.14", "54.69", "53.03", "54.69", "33.19", "53.03", "33.19", "31.04", "14.94", "18.13"], ["Glossoscolex sp.", "88.17", "87.55", "88.17", "73.82", "73.67", "73.82", "65.22", "73.67", "65.22", "59.75", "49.91", "33.55"], ["Haplotaxis gordioides", "86.63", "89.16", "86.63", "69.18", "69.65", "69.18", "45.94", "69.65", "45.94", "42.19", "30.48", "21.58"], ["?Haplotaxidae sp.", "81.18", "86.38", "-----", "55.95", "54.58", "-----", "31.37", "54.58", "-----", "22.63", "-----", "-----"], ["Hemigastrodrilus monicae", "74.66", "73.40", "74.66", "47.84", "42.08", "47.84", "28.08", "42.08", "28.08", "22.91", "6.14", "14.72"], ["Hormogaster elisae", "61.55", "61.14", "61.55", "40.13", "35.46", "40.13", "22.07", "35.46", "22.07", "18.66", "1.57", "15.17"], ["Kerriona sp. Graciosa1", "79.62", "77.63", "79.62", "68.83", "69.86", "68.83", "46.30", "69.86", "46.30", "44.66", "32.04", "16.78"], ["Komarekiona eatoni", "75.54", "78.33", "75.54", "49.28", "46.41", "49.28", "30.93", "46.41", "30.93", "29.50", "14.06", "19.33"], ["Kynotus pittarelli", "78.34", "80.98", "78.34", "48.40", "44.51", "48.40", "31.88", "44.51", "31.88", "33.44", "19.32", "20.93"], ["Lumbriculus variegatus", "84.69", "86.95", "-----", "62.91", "63.29", "-----", "44.54", "63.29", "-----", "45.40", "34.07", "33.20"], ["Lutodrilus multivesiculatus", "78.23", "77.77", "78.23", "50.82", "47.41", "50.82", "27.34", "47.41", "27.34", "23.54", "6.18", "18.38"], ["Maoridrilus wilkini", "86.86", "86.10", "86.86", "75.28", "75.10", "75.28", "60.26", "75.10", "60.26", "54.11", "43.85", "35.90"], ["Microchaetidae sp.", "79.37", "80.11", "79.37", "48.98", "43.78", "48.98", "28.13", "43.78", "28.13", "24.11", "7.76", "15.32"], ["Microchaetus sp.", "74.62", "75.20", "74.62", "45.96", "42.02", "45.96", "27.69", "42.02", "27.69", "26.44", "9.31", "14.77"], ["Parachilota sp.", "73.61", "72.09", "73.61", "59.08", "58.99", "59.08", "42.15", "58.99", "42.15", "32.77", "17.19", "25.94"], ["Pelodrilus sp.", "75.31", "79.76", "75.31", "50.98", "50.45", "50.98", "32.80", "50.45", "32.80", "35.99", "21.16", "16.93"], ["Place Kabary 2 sp.", "70.17", "68.40", "70.17", "49.41", "49.91", "49.41", "23.89", "49.91", "23.89", "23.47", "6.43", "18.58"], ["Pontodrilus litoralis", "66.37", "66.34", "66.37", "46.87", "46.53", "46.87", "26.84", "46.53", "26.84", "19.66", "2.16", "15.92"], ["Propappus volki", "77.03", "81.59", "-----", "56.39", "57.47", "-----", "36.90", "57.47", "-----", "36.68", "22.49", "15.02"], ["Rhinodrilus priollii", "75.00", "76.10", "75.00", "45.59", "43.06", "45.59", "24.06", "43.06", "24.06", "26.27", "9.64", "16.17"], ["Scherotheca savignyi", "76.55", "75.20", "76.55", "54.39", "49.26", "54.39", "30.39", "49.26", "30.39", "28.99", "12.94", "14.67"], ["Sparganophilus sp.", "68.43", "71.47", "68.43", "36.25", "32.65", "36.25", "21.49", "32.65", "21.49", "23.05", "7.09", "13.37"], ["Urobenus brasiliensis", "84.07", "85.13", "84.07", "59.66", "56.92", "59.66", "39.04", "56.92", "39.04", "37.79", "23.41", "24.69"], ["Vignysa popi", "86.01", "84.87", "86.01", "69.72", "66.08", "69.72", "50.88", "66.08", "50.88", "51.03", "39.39", "21.53"]], "row_count": 42, "column_count": 13, "numeric_cells": 482, "header_rows": 2, "locator": "section[13]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:28558722:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:45e6e960217f79fbd7b5713c9ccacea162d7d1d758d91a36ce46e12a97704915", "bytes": 903, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#Tab4", "version": null, "note": "PhyloBayes divergence time estimates (mean ± standard error) in millions of years ago for three data matrices for two key nodes in the earthworm radiation—the node separating Kynotus from Sparganophilus + Komarekiona (node 1, Fig. 1) and the node separating the Northern Hemisphere clade comprising Lutodrilus and Lumbricoidea and the clade comprising Southern Hemisphere representatives of several families (node 2, Fig. 1)", "structure": {"pmcid": "PMC5450073", "section_index": 16, "section_title": "Divergence times", "row_count": 4, "column_count": 3}, "table": {"label": "Table 4", "caption": "PhyloBayes divergence time estimates (mean ± standard error) in millions of years ago for three data matrices for two key nodes in the earthworm radiation—the node separating Kynotus from Sparganophilus + Komarekiona (node 1, Fig. 1) and the node separating the Northern Hemisphere clade comprising Lutodrilus and Lumbricoidea and the clade comprising Southern Hemisphere representatives of several families (node 2, Fig. 1)", "rows": [["Data Matrix", "Node 1 (mean ± SE)", "Node 2 (mean ± SE)"], ["75% with ?Haplotaxidae sp., unfiltered", "164.527 ± 22.2868", "161.104 ± 21.0178"], ["no ?Haplotaxidae sp., filtered, all sites", "186.1521 ± 23.2339", "186.0185 ± 22.18"], ["no ?Haplotaxidae sp., filtered, no >50% gaps", "178.1059 ± 21.9198", "177.6679 ± 21.1014"]], "row_count": 4, "column_count": 3, "numeric_cells": 10, "header_rows": 1, "locator": "section[16]/table-wrap[1]#Tab4"}}], "gaps": ["asset:data:geo:PRJDB3115 not downloaded", "asset:data:geo:PRJDB3115 licence not read", "asset:data:geo:PRJNA196484 not downloaded", "asset:data:geo:PRJNA196484 licence not read", "asset:data:geo:PRJNA362879 not downloaded", "asset:data:geo:PRJNA362879 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "SOWH test and Bayesian topology test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "both a SOWH test and a Bayesian topology test strongly reject Dichogaster monophyly."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 75.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (SOWH test and Bayesian topology test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PRJNA362879", "PRJNA196484", "PRJDB3115"], "resolved_accessions": [], "statements": ["The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71)."], "basis": "The paper names PRJNA362879, PRJNA196484, PRJDB3115, but the accession does not resolve in the repository (not_in_ncbi_bioproject, not_in_ncbi_bioproject, not_in_ncbi_bioproject), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28558722", "data:geo:PRJDB3115", "asset:table:pmid:28558722:1", "asset:table:pmid:28558722:2", "asset:table:pmid:28558722:3", "asset:table:pmid:28558722:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PRJDB3115"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:12Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 161864, "completion_tokens": 5787, "cached_tokens": 1824}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:28558722", "type": "paper", "label": "pmid:28558722"}, {"id": "source:pmid:28558722", "type": "manuscript", "label": "PMID 28558722 full text"}, {"id": "data:geo:PRJDB3115", "type": "dataset", "label": "GEO PRJDB3115"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28558722", "type": "paper", "label": "pmid:28558722"}, {"id": "source:pmid:28558722", "type": "manuscript", "label": "PMID 28558722 full text"}, {"id": "data:geo:PRJDB3115", "type": "dataset", "label": "GEO PRJDB3115"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28558722", "type": "extraction", "used": ["source:pmid:28558722"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PRJDB3115", "type": "accession_resolution", "used": ["data:geo:PRJDB3115"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:28558722", "parent_hash": "sha256:e2fb6a9f077d8ea006ce61eebd4877ac2cf899c26404e0a84bb35a83e7faff60", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PRJDB3115 licence not read", "asset:data:geo:PRJDB3115 not downloaded", "asset:data:geo:PRJNA196484 licence not read", "asset:data:geo:PRJNA196484 not downloaded", "asset:data:geo:PRJNA362879 licence not read", "asset:data:geo:PRJNA362879 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:24:39+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}